Being curious I asked this question on Wayland's developper mailing list and Pekka Paalanen (many thanks to him) answered quickly:
- to bind actions to the 'pause' key, this would be a DE specific configuration.
- for the fullscreen transparent Window letting mouse events pass through it: this is possible in Wayland as Wayland clients can define their input region, so when not drawing the input region would be empty, when drawing it would cover the fullscreen.
So Gromit should be possible on Wayland, the only issue is that it would require a DE specific configuration for the keyboard.